Interplay between chromophore binding and domain assembly by the B(12)-dependent photoreceptor protein, CarH

Organisms across the natural world respond to their environment through the action of photoreceptor proteins. The vitamin B(12)-dependent photoreceptor, CarH, is a bacterial transcriptional regulator that controls the biosynthesis of carotenoids to protect against photo-oxidative stress. The binding of B(12) to CarH monomers in the dark results in the formation of a homo-tetramer that complexes with DNA; B(12) photochemistry results in tetramer dissociation, releasing DNA for transcription. Although the details of the response of CarH to light are beginning to emerge, the biophysical mechanism of B(12)-binding in the dark and how this drives domain assembly is poorly understood. Here – using a combination of molecular dynamics simulations, native ion mobility mass spectrometry and time-resolved spectroscopy – we reveal a complex picture that varies depending on the availability of B(12). When B(12) is in excess, its binding drives structural changes in CarH monomers that result in the formation of head-to-tail dimers. The structural changes that accompany these steps mean that they are rate-limiting. The dimers then rapidly combine to form tetramers. Strikingly, when B(12) is scarcer, as is likely in nature, tetramers with native-like structures can form without a B(12) complement to each monomer, with only one apparently required per head-to-tail dimer. We thus show how a bulky chromophore such as B(12) shapes protein/protein interactions and in turn function, and how a protein can adapt to a sub-optimal availability of resources. This nuanced picture should help guide the engineering of B(12)-dependent photoreceptors as light-activated tools for biomedical applications.